De novo assembly

owlbike · 02-27-2019, 11:03 PM

hello everyone,

I have recently started working in a lab and have been assigned the following task.

AIM:To assemble the given sequences as one consensus for transformation to be even more specific. Looking for regions around trnA, trnI, 23s and 16s.

Data I have:
1) chloroplast genome sequence of an algae along with its circular map.

2) Sequences of the Primers used. Three sets of primers have been used (forward and reverse) along with trnaI and trnaA (both forward and reverse).
The sequences are in ".ab1" format.

Please let me know how will you approach this problem.

PS: No other files or data has been handed over to me. Its someone else's work and that person has left.

pmiguel · 03-01-2019, 03:53 AM

Upon being given such a homework assignment, I would post it on appropriate web forums hoping to find someone gullible enough to save me from answering the question myself.

Wait, no! I would not do that. But you did, didn't you?
--
Phillip

owlbike · 03-01-2019, 04:08 AM

@pmiguel No, I didn't post any homework question. I framed it in a way (in points ) so that it becomes easier for everyone to understand and they can guide me. I have recently joined a lab and have been given someone's unfinished work with no complete data.

pmiguel · 03-01-2019, 07:21 AM

"You have recently started working in a lab and have been assigned the following task:"

That was the first sentence of your homework question (or take home exam), right?

--
Phillip

owlbike · 03-16-2019, 02:21 AM

yes that was the first line. Had to restate it because it seemed you missed it. If you can't help budding people in science you may not answer anything at all.

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02-27-2019, 11:03 PM	#1
owlbike Junior Member Location: delhi Join Date: Feb 2019 Posts: 4	De novo assembly hello everyone, I have recently started working in a lab and have been assigned the following task. AIM:To assemble the given sequences as one consensus for transformation to be even more specific. Looking for regions around trnA, trnI, 23s and 16s. Data I have: 1) chloroplast genome sequence of an algae along with its circular map. 2) Sequences of the Primers used. Three sets of primers have been used (forward and reverse) along with trnaI and trnaA (both forward and reverse). The sequences are in ".ab1" format. Please let me know how will you approach this problem. PS: No other files or data has been handed over to me. Its someone else's work and that person has left.

03-01-2019, 03:53 AM	#2
pmiguel Senior Member Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008 Posts: 2,317	Upon being given such a homework assignment, I would post it on appropriate web forums hoping to find someone gullible enough to save me from answering the question myself. Wait, no! I would not do that. But you did, didn't you? -- Phillip

03-01-2019, 04:08 AM	#3
owlbike Junior Member Location: delhi Join Date: Feb 2019 Posts: 4	@pmiguel No, I didn't post any homework question. I framed it in a way (in points ) so that it becomes easier for everyone to understand and they can guide me. I have recently joined a lab and have been given someone's unfinished work with no complete data.

03-01-2019, 07:21 AM	#4
pmiguel Senior Member Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008 Posts: 2,317	"You have recently started working in a lab and have been assigned the following task:" That was the first sentence of your homework question (or take home exam), right? -- Phillip

03-16-2019, 02:21 AM	#5
owlbike Junior Member Location: delhi Join Date: Feb 2019 Posts: 4	yes that was the first line. Had to restate it because it seemed you missed it. If you can't help budding people in science you may not answer anything at all.